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= Introduction =
Here are examples of what you can do with ZINC15, organized by [[ZINC15:Levels]].


[[ZINC15:examples:abstract]]
= Public Access =
[[ZINC15:examples:introduction]]
* [[ZINC15:examples:public]]
* [[ZINC15:videos]]  
* [[ZINC15:examples:screening]]  


== Results  ==
query ZINC using api
[[ZINC15:examples:results-tables]]
time wget --user gpcr --password xtal -O - "http://zinc15.docking.org/substances.txt:smiles,zinc_id,purchasability?
purchasability:gt=10&mwt:le=350&mwt:gt=50&logp:le=3.5&structure.num_rotatable_bonds:le=7&structure:contains=[C;D1]%3D[CD3]C(%3DO)OC&count=all" | tee 18.txt | cat -n


[[ZINC15:examples:results-figures]]


[[ZINC15-examples:results-text]]
= Private access =  
 
These require ssh access or a private copy of ZINC
== ZINC15 Actions ==
* [[ZINC15:examples:private]]
[[ZINC15:Actions]]
 
= Examples organized by topic =
== ligands for genes ==
[[ZINC15:examples:genes]]
 
== metabolites and natural products ==
[[ZINC15:examples:biogenic]]
 
== drugs and bioactives ==
[[ZINC15:examples:bioactive]]
 
== purchasable screening libraries ==
[[ZINC15:examples:screening]]
 
= Examples organized by level of difficulty =
See [[ZINC15:Levels]] for a description of our classification of questions by how easy it is to answer them.
== Public access ==
* [[ZINC15:examples:level1]] - questions that are easy to answer using the [zinc15.docking.org zinc15.docking.org] web page.
* [[ZINC15:examples:level2]] - questions that require you compose your own query in the URL. This is usually because we have not yet gotten around to writing a graphical interface for this class of questions.
* [[ZINC15:examples:level3]] - these are questions that are difficult or not possible to answer using the ZINC 15 website as it currently exists, but can be answered using a bit of python. We show you how.  Using a bit of python can dramatically extend the power of the ZINC website.
 
== Private access required ==
* [[ZINC15:examples:level4]] - these (and all higher levels) require privileged access to ZINC which is not available to the general public. However, by showing you what these questions are, and how you can solve them with access, we alert you to the possibilities of ZINC. Ask us if you require this level of access to ZINC.
* [[ZINC15:examples:level5]] - higher level access. not just privileged ipynb, but also command line ZINC shell.
* [[ZINC15:examples:level6]] - SQL
* [[ZINC15:examples:level7]] - SQL and python
* [[ZINC15:examples:level8]] - questions we've been asked that we are unable to answer as this time.
 
zinc15.docking.org/substances.txt:smiles,zinc_id,tanimoto_similarity?
catalog.purchasable%20gt%209&ecfp4.data%20similarto%20CC(=O)Oc1ccccc1C(=O)O%20within%20.5?count=all
 
[http://youtube.com/chemistry4biology YouTube]
 
[http://ipynb.docking.org iPython Notebooks]
 
 
= How many primary amines are available for sale in preparative quantities? =
URL="zinc15.docking.org:8015/substances.txt?substance.structure:contains=[ND1]&catalog.bb=True&substance.purchasability:gt=9&count=all"
wget -o log -O amines.smi "$URL"
wc -l amines.smi
answer: xxxx
 
= How many ChEMBL targets have at least one purchasable compound for sale? =
zinc15.docking.org:8015/activities:target.uniprot?catalog.purchasable .....
 
= How many ligands for class F GPCRs are for sale? =
zinc15.docking.org:8015/substances.txt:smiles,sub_id,gene.name?subclass=name=GPCR-F&substance.purchasability:ge=10&count=all
 
= What is the nearest metabolite or drug to my compound? =
zinc15.docking.org/substances.txt?ecfp4.data:tanimoto,0.5=<url-encoded-smiles>
thus for ZINC27,
zinc15.docking.org/substances.txt?ecfp4.data:tanimoto,0.5=N[C@@H](CCc1ccc(N(CCCl)CCCl)cc1)C(=O)O
 
= Which FDA approved drugs are also metabolites? =
zinc15.docking.org/substances?substance.features:contains=211,202&count=all
 
 
== “Which compounds are in Drugbank but not in ChEMBL Drugstore? ==
 
 
== Which genes have a ligand reported that binds at 10nM concentration or better? ==
zinc15.docking.org:8015/activities.txt:gene.name?activities.affinitynm:ge=8&distinct=gene.name&count=all
 
== Which targets do hydroxamic acids bind to? ==
zinc15.docking.org/targets.txt:target.uniprot?structure.contains=C(=O)[ND2][OD1]&distinct=target.uniprot&count=all
 
== Which vendors sell the most biogenic compounds (natural products), and what are those compounds? ==
zinc15.docking.org/catitms.txt:catalog.short_name,catitm.supplier_code,substance.zinc_id,substance.smiles?catalog.np=1&count=all
 
== How many primary amines as for sale in preparative quantitites? ==
zinc15.docking.org/substances.txt?substance.structure:contains=[ND1]&catalog.bb=True&count=all


[[Category:Tutorials]]
[[Category:ZINC15]]
[[Category:ZINC15]]
[[Category:Idioms]]

Latest revision as of 17:34, 17 August 2017

Introduction

Here are examples of what you can do with ZINC15, organized by ZINC15:Levels.

Public Access

query ZINC using api 

time wget --user gpcr --password xtal -O - "http://zinc15.docking.org/substances.txt:smiles,zinc_id,purchasability?
purchasability:gt=10&mwt:le=350&mwt:gt=50&logp:le=3.5&structure.num_rotatable_bonds:le=7&structure:contains=[C;D1]%3D[CD3]C(%3DO)OC&count=all" | tee 18.txt | cat -n


Private access

These require ssh access or a private copy of ZINC

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